A gene-driven ENU-based approach to generating an allelic series in any gene

N-ethyl-N-nitrosourea (ENU) introduces mutations throughout the mouse genome at relatively high efficiency. Successful high-throughput phenotype screens have been reported and alternative screens using sequence-based approaches have been proposed. For the purpose of generating an allelic series in selected genes by a sequence-based approach, we have constructed an archive of over 4000 DNA samples from individual F₁ ENU-mutagenized mice paralleled by frozen sperm samples. Together with our previously reported archive, the total size now exceeds 6000 individuals. A gene-based screen of 27.4 Mbp of DNA, carried out using denaturing high-performance liquid chromatography (DHPLC), found a mutation rate of 1 in 1.01 Mbp of which 1 in 1.82 Mbp were potentially functional. Screening of whole or selected regions of genes on subsets of the archive has allowed us to identify 15 new alleles from 9 genes out of 15 tested. This is a powerful adjunct to conventional mutagenesis strategies and has the advantage of generating a variety of alleles with potentially different phenotypic outcomes that facilitate the investigation of gene function. It is now available to academic collaborators as a community resource.     

Neuroprotection in a Novel Mouse Model of Multiple Sclerosis

Multiple sclerosis is an immune-mediated, demyelinating and neurodegenerative disease that currently lacks any neuroprotective treatments. Innovative neuroprotective trial designs are required to hasten the translational process of drug development. An ideal target to monitor the efficacy of strategies aimed at treating multiple sclerosis is the visual system, which is the most accessible part of the human central nervous system. A novel C57BL/6 mouse line was generated that expressed transgenes for a myelin oligodendrocyte glycoprotein-specific T cell receptor and a retinal ganglion cell restricted-Thy1 promoter-controlled cyan fluorescent protein. This model develops spontaneous or induced optic neuritis, in the absence of paralytic disease normally associated with most rodent autoimmune models of multiple sclerosis. Demyelination and neurodegeneration could be monitored longitudinally in the living animal using electrophysiology, visual sensitivity, confocal scanning laser ophthalmoscopy and optical coherence tomography all of which are relevant to human trials. This model offers many advantages, from a 3Rs, economic and scientific perspective, over classical experimental autoimmune encephalomyelitis models that are associated with substantial suffering of animals. Optic neuritis in this model led to inflammatory damage of axons in the optic nerve and subsequent loss of retinal ganglion cells in the retina. This was inhibited by the systemic administration of a sodium channel blocker (oxcarbazepine) or intraocular treatment with siRNA targeting caspase-2. These novel approaches have relevance to the future treatment of neurodegeneration of MS, which has so far evaded treatment.     

Carbon Inputs from <Emphasis Type="Italic">Miscanthus</Emphasis> Displace Older Soil Organic Carbon Without Inducing Priming

The carbon (C) dynamics of a bioenergy system are key to correctly defining its viability as a sustainable alternative to conventional fossil fuel energy sources. Recent studies have quantified the greenhouse gas mitigation potential of these bioenergy crops, often concluding that C sequestration in soils plays a primary role in offsetting emissions through energy generation. Miscanthus is a particularly promising bioenergy crop and research has shown that soil C stocks can increase by more than 2 t C ha^?1 yr^?1. In this study, we use a stable isotope (¹³C) technique to trace the inputs and outputs from soils below a commercial Miscanthus plantation in Lincolnshire, UK, over the first 7 years of growth after conversion from a conventional arable crop. Results suggest that an unchanging total topsoil (0–30 cm) C stock is caused by Miscanthus additions displacing older soil organic matter. Further, using a comparison between bare soil plots (no new Miscanthus inputs) and undisturbed Miscanthus controls, soil respiration was seen to be unaffected through priming by fresh inputs or rhizosphere. The temperature sensitivity of old soil C was also seen to be very similar with and without the presence of live root biomass. Total soil respiration from control plots was dominated by Miscanthus-derived emissions with autotrophic respiration alone accounting for ～50 % of CO₂. Although total soil C stocks did not change significantly over time, the Miscanthus-derived soil C accumulated at a rate of 860 kg C ha^?1 yr^?1 over the top 30 cm. Ultimately, the results from this study indicate that soil C stocks below Miscanthus plantations do not necessarily increase during the first 7 years.     

Impacts of natural factors and farming practices on greenhouse gas emissions in the North China Plain: A meta‐analysis

Requirements for mitigation of the continued increase in greenhouse gas (GHG ) emissions are much needed for the North China Plain (NCP ). We conducted a meta‐analysis of 76 published studies of 24 sites in the NCP to examine the effects of natural conditions and farming practices on GHG emissions in that region. We found that N₂O was the main component of the area‐scaled total GHG balance, and the CH ₄ contribution was <5%. Precipitation, temperature, soil pH , and texture had no significant impacts on annual GHG emissions, because of limited variation of these factors in the NCP . The N₂O emissions increased exponentially with mineral fertilizer N application rate, with y  =  0.2389e^0.0058x for wheat season and y  =  0.365e^0.0071x for maize season. Emission factors were estimated at 0.37% for wheat and 0.90% for maize at conventional fertilizer N application rates. The agronomic optimal N rates (241 and 185 kg N ha^?1 for wheat and maize, respectively) exhibited great potential for reducing N₂O emissions, by 0.39 (29%) and 1.71 (56%) kg N₂O‐N ha^?1 season^?1 for the wheat and maize seasons, respectively. Mixed application of organic manure with reduced mineral fertilizer N could reduce annual N₂O emissions by 16% relative to mineral N application alone while maintaining a high crop yield. Compared with conventional tillage, no‐tillage significantly reduced N₂O emissions by ~30% in the wheat season, whereas it increased those emissions by ~10% in the maize season. This may have resulted from the lower soil temperature in winter and increased soil moisture in summer under no‐tillage practice. Straw incorporation significantly increased annual N₂O emissions, by 26% relative to straw removal. Our analysis indicates that these farming practices could be further tested to mitigate GHG emission and maintain high crop yields in the NCP .     

Benchmarking the effects of operating system interference on extreme-scale parallel machines

We investigate operating system noise, which we identify as one of the main reasons for a lack of synchronicity in parallel applications. Using a microbenchmark, we measure the noise on several contemporary platforms and find that, even with a general-purpose operating system, noise can be limited if certain precautions are taken. We then inject artificially generated noise into a massively parallel system and measure its influence on the performance of collective operations. Our experiments indicate that on extreme-scale platforms, the performance is correlated with the largest interruption to the application, even if the probability of such an interruption on a single process is extremely small. We demonstrate that synchronizing the noise can significantly reduce its negative influence.